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Ensembl Variation - Data description

Below is a description of the data we store in the databases for Ensembl Variation.
For several different species in Ensembl, we import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to a quality control process to flag suspect data.
We classify the variants into different classes and calculate the predicted consequence(s) of the variant and we have also created variation sets to help people retrieve a specific group of variants from a particular dataset.
In human, we calculate the linkage disequilibrium for each variant, by population.

See some examples of imported data on the Ensembl website (Human):

  • Location of a variation in the genome
  • Population genotypes and frequencies of a variation
  • Individual genotypes of a variation
  • Sample information and frequencies of a somatic variant
  • Phenotype(s) associated with a variation
  • Citations

Variation species and data types

The Ensembl Variation database stores data imported from external sources and also data calculated on site.

  • Data imported from external sources (dbSNP, Sanger, DGVa, ...):
    • Variations (SNPs, in-dels, insertion, deletion, ...)
    • Structural variations (copy number variation, tandem duplication, inversion, ...)
    • Probes for copy number variations
    • Locations for variations and structural variations
    • Alleles
    • Populations
    • Genotypes
    • Phenotypes (e.g. list of phenotypes in human)
    • Citations (extracted from dbSNP submissions and text mining performed by EPMC and UCSC)
  • Calculated data: see the Predicted data page.

Ensembl stores variation data for the following species, but note that users can still use the Variant Effect Predictor VEP on species for which we do not currently have a variation database.

There are currently 22 variation databases in Ensembl:

SpeciesSequence variant count Structural variantGenotype - IndividualGenotype - PopulationPhenotypeCitationSIFTPolyPhen
Bos taurus
> 73 millions variants -
Canis familiaris
> 3 millions variants -
Danio rerio
> 1 million variants - -
Drosophila melanogaster
> 6 millions variants - - - - -
Equus caballus
> 4 millions variants - -
Felis catus
> 327,000 variants - - - - - -
Gallus gallus
> 9 millions variants - -
Homo sapiens
> 64 millions variants
Macaca mulatta
> 3 millions variants - - -
Meleagris gallopavo
> 9,000 variants - - - - -
Monodelphis domestica
> 1 million variants - - - - - - -
Mus musculus
> 71 millions variants -
Nomascus leucogenys
> 1 million variants - - - - - -
Ornithorhynchus anatinus
> 1 million variants - - - - -
Ovis aries
> 32 millions variants - - -
Pan troglodytes
> 1 million variants - - - -
Pongo abelii
> 10 millions variants - - - - - -
Rattus norvegicus
> 5 millions variants - -
Saccharomyces cerevisiae
> 263,000 variants - - - - -
Sus scrofa
> 28 millions variants -
Taeniopygia guttata
> 1 million variants - - - - -
Tetraodon nigroviridis
> 902,000 variants - - - - - - -

The full list of species and their assembly versions in Ensembl is available here.


The majority of variants are imported from NCBI dbSNP. The data is imported when it is released by dbSNP and incorporated into the next Ensembl release. If dbSNP releases the data on a different assembly, Ensembl will remap the variant positions onto the current assembly. Data from projects like the HapMap Project and 1000 Genomes Project is imported once it has been submitted to dbSNP.

Ensembl also includes data from other sources. To view data from these sources in the browser go to a species Location page (e.g. for human), and click on the 'Configure this page' link on the left-hand side. The 'Variation' and 'Somatic mutations' sections contain a track list of all sources of variation data for that species.


Variation displays

Variation data can be viewed in the browser through pages such as:

  • Gene: Variation Table and Variation Image (for all variations in a gene) e.g. for all variants in KCNE2. Structural Variation to see all structural variants overlapping the gene.
  • Transcript: Population comparison, Comparison image (for comparing variants in a transcript across different individual or strain sequences) e.g. compare Tmco4 in different mouse strains
  • Transcript: Sequence, protein: list of the coding variants in protein coordinates.
  • Location: Region in Detail (Variations can be drawn using "Configure this page" at the left. The menu allows display of information in Ensembl databases along with external sources in DAS format such as DGV loci.)
  • Phenotype: A karyotype view to display the variants associated with a certain phenotype, e.g. phenotype "Glaucoma".

Clicking on any variation on an Ensembl page will open a Variation tab with information about the flanking sequence and source for the selected variation. Links to linkage disequilibrium (LD) plots, phenotype information (for human) from EGA, OMIM and NHGRI and Ensembl genes and transcripts that include the variation can be found at the left of this tab. You may also view multiple genome alignments of various species, highlighting the variation. Ancestral sequences are included in this display.

Variation information can also be accessed using BioMart (gene or variation database), and the Perl API (variation API).


Variation classes

We call the class of a variation according to its component alleles and its mapping to the reference genome, and then display this information on the website. Internally we use Sequence Ontology terms, but we map these to our own 'display' terms where common usage differs from the SO definition (e.g. our term SNP is closer to the SO term SNV). All the classes we call, along with their equivalent SO term are shown in the table below. We also differentiate somatic mutations from germline variations in the display term, prefixing the term with 'somatic'. API users can fetch either the SO term or the display term.


* SO term SO description SO accession Ensembl term Called for
SNV SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. SO:0001483 SNP Variation
somatic_SNV
genetic_marker A measurable sequence feature that varies within a population. SO:0001645 genetic_marker Variation
somatic_genetic_marker
indel A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. SO:1000032 indel Variation
somatic_indel
substitution A sequence alteration where the length of the change in the variant is the same as that of the reference. SO:1000002 substitution Variation
somatic_substitution
tandem_repeat Two or more adjcent copies of a region (of length greater than 1). SO:0000705 tandem_repeat Variation
somatic_tandem_repeat
complex_structural_alteration A structural sequence alteration or rearrangement encompassing one or more genome fragments. SO:0001784 Complex Structural variation
somatic_Complex
copy_number_gain A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. SO:0001742 Gain Structural variation
somatic_Gain
copy_number_loss A sequence alteration whereby the copy number of a given region is less than the reference sequence. SO:0001743 Loss Structural variation
somatic_Loss
copy_number_variation A variation that increases or decreases the copy number of a given region. SO:0001019 CNV Structural variation
somatic_CNV
duplication An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. SO:1000035 Duplication Structural variation
somatic_Duplication
interchromosomal_breakpoint A rearrangement breakpoint between two different chromosomes. SO:0001873 Interchromosomal breakpoint Structural variation
somatic_Interchromosomal breakpoint
intrachromosomal_breakpoint A rearrangement breakpoint within the same chromosome. SO:0001874 Intrachromosomal breakpoint Structural variation
somatic_Intrachromosomal breakpoint
inversion A continuous nucleotide sequence is inverted in the same position. SO:1000036 inversion Structural variation
somatic_inversion
mobile_element_insertion A kind of insertion where the inserted sequence is a mobile element. SO:0001837 Mobile element insertion Structural variation
somatic_Mobile element insertion
novel_sequence_insertion An insertion the sequence of which cannot be mapped to the reference genome. SO:0001838 Novel sequence insertion Structural variation
somatic_Novel sequence insertion
tandem_duplication A duplication consisting of 2 identical adjacent regions. SO:1000173 Tandem duplication Structural variation
somatic_Tandem duplication
translocation A region of nucleotide sequence that has translocated to a new position. SO:0000199 translocation Structural variation
somatic_translocation
deletion The point at which one or more contiguous nucleotides were excised. SO:0000159 deletion Variation
Structural variation
somatic_deletion
insertion The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. SO:0000667 insertion Variation
Structural variation
somatic_insertion
sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. SO:0001059 sequence_alteration Variation
Structural variation
somatic_sequence_alteration
probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. SO:0000051 CNV_PROBE CNV probe

* Corresponding colours for the Ensembl web displays (only for Structural variations). The colours are based on the dbVar displays.

Human Variation class distribution - Ensembl 77


Insertion and Deletion coordinates

In Ensembl, an insertion is indicated by start coordinate = end coordinate + 1. For example, an insertion of 'C' between nucleotides 12600 and 12601 on the forward strand is indicated with start and end coordinates as follows:

   12601     12600   

A deletion is indicated by the exact nucleotide coordinates. For example, a three base pair deletion of nucleotides 12600, 12601, and 12602 of the reverse strand will have start and end coordinates of :

   12600     12602    

Populations

For each variant we store population data (allele frequencies, genotypes) available from different projects (e.g. 1000 Genomes, HapMap). You can see this on our variation pages, for example: rs699.
Below we list the population names associated with the 1000 Genomes Project, the HapMap Project and the ESP project:

Populations from the 1000 Genomes Project (Human)

Name Size Description
1000GENOMES:phase_1_AFR 246 All African individuals from phase 1 of the 1000 Genomes Project (YRI, LWK, ASW)
1000GENOMES:phase_1_ALL 1092 All individuals from phase 1 of the 1000 Genomes Project
1000GENOMES:phase_1_AMR 181 All American individuals from phase 1 of the 1000 Genomes Project
1000GENOMES:phase_1_ASN 286 All East Asian individuals from phase 1 of the 1000 Genomes Project (CHB, JPT, CHS)
1000GENOMES:phase_1_ASW 61 Americans of African Ancestry in SW USA
1000GENOMES:phase_1_CEU 85 Utah Residents (CEPH) with Northern and Western European ancestry
1000GENOMES:phase_1_CHB 97 Han Chinese in Bejing, China
1000GENOMES:phase_1_CHS 100 Southern Han Chinese
1000GENOMES:phase_1_CLM 60 Colombian from Medellin, Colombia
1000GENOMES:phase_1_EUR 379 All European individuals from phase 1 of the 1000 Genomes Project (CEU, TSI, FIN, GBR, IBS)
1000GENOMES:phase_1_FIN 93 Finnish in Finland
1000GENOMES:phase_1_GBR 89 British in England and Scotland
1000GENOMES:phase_1_IBS 14 Iberian population in Spain
1000GENOMES:phase_1_JPT 89 Japanese in Tokyo, Japan
1000GENOMES:phase_1_LWK 97 Luhya in Webuye, Kenya
1000GENOMES:phase_1_MXL 66 Mexican Ancestry from Los Angeles USA
1000GENOMES:phase_1_PUR 55 Puerto Ricans from Puerto Rica
1000GENOMES:phase_1_TSI 98 Toscani in Italy
1000GENOMES:phase_1_YRI 88 Yoruba in Ibadan, Nigera

Variants which have been discovered in this project have the "evidence status" 1000Genomes. On the website this corresponds to the icon .

Populations from the HapMap Project (Human)

Name Size Description
CSHL-HAPMAP:HAPMAP-ASW 90 African ancestry in Southwest USA. ASW is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HapMap-CEU 185 Utah residents with Northern and Western European ancestry from the CEPH collection. CEU is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-CHB 90 Han Chinese in Beijing, China. CHB is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-CHD 100 Chinese in Metropolitan Denver, Colorado. CHD is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-GIH 100 Gujarati Indians in Houston, Texas. GIH is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HapMap-HCB 48 45 unrelated Han Chinese in Beijing, China, representing one of the populations studied in the International HapMap project ( http://www.hapmap.org). See http://www.hapmap.org/citinghapmap.html.en for further information about,this population and others studied in the project. http://www.hapmap.org/hapmappopulations.html.en,also has relevant information.
CSHL-HAPMAP:HapMap-JPT 93 Japanese in Tokyo, Japan. JPT is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-LWK 100 Luhya in Webuye, Kenya. LWK is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-MEX 90 Mexican ancestry in Los Angeles, California. MEX is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-MKK 180 Maasai in Kinyawa, Kenya. MKK is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HAPMAP-TSI 100 Toscans in Italy. TSI is one of the 11 populations in HapMap phase 3.
CSHL-HAPMAP:HapMap-YRI 185 Yoruba in Ibadan, Nigeria. YRI is one of the 11 populations in HapMap phase 3.

Variants which have been discovered in this project have the "evidence status" HapMap. On the website this corresponds to the icon .

Populations from the Exome Sequencing Project (ESP) (Human)

Name Size Description
ESP6500:African_American - -
ESP6500:European_American - -

Variants which have been discovered in this project have the "evidence status" ESP. On the website this corresponds to the icon .

Note: This population data is stored in the population table of the Variation database. You can see a description of the population table here.


Variation sets

We use the concept of variation sets to group variations that share some property together. For example, we have grouped the variations identified in the three different 1000 Genomes pilot studies into separate variation sets. The sets can be further subdivided into supersets and subsets to reflect hierarchical relationships between them. In the case of the 1000 Genomes phase 1 sets, these are divided into subsets based on population. For example, the set representing variations identified in the 1000 Genomes phase 1 study is named '1000 Genomes - All' and has several subsets like: '1000 Genomes - AFR', '1000 Genomes - AMR', '1000 Genomes - ASN' and '1000 Genomes - EUR'. The variation sets can be displayed as separate tracks on the location view. This behaviour is controlled from the 'Variation' section on the configuration panel which is accessed by clicking the 'Configure this page' link in the left hand side navigation.

The sets are constructed during production and are stored in the database. The table below lists the available variation sets in the Ensembl variation database (subsets are indicated by bullet points).

Variation sets common to all species

Name Short name Description
All failed variations fail_all Variations that have failed the Ensembl QC checks

Variation sets specific to Human

Name Short name Description
1000 Genomes - All 1kg Variants genotyped by the 1000 Genomes project (phase 1)
  • 1000 Genomes - AFR
1kg_afr Variants genotyped in African individuals by the 1000 Genomes project (phase 1)
  • 1000 Genomes - AFR - common
1kg_afr_com Variants genotyped in African individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
  • 1000 Genomes - AMR
1kg_amr Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1)
  • 1000 Genomes - AMR - common
1kg_amr_com Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
  • 1000 Genomes - ASN
1kg_asn Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1)
  • 1000 Genomes - ASN - common
1kg_asn_com Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
  • 1000 Genomes - All - common
1kg_com Variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1%
  • 1000 Genomes - EUR
1kg_eur Variants genotyped in European individuals by the 1000 Genomes project (phase 1)
  • 1000 Genomes - EUR - common
1kg_eur_com Variants genotyped in European individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
1000 Genomes - High coverage - Trios 1kg_hct Variations called by the 1000 Genomes project on high coverage sequence data from two family trios (Pilot 2)
1000 Genomes - High quality 1kg_hq Structural variants labelled as "High quality site" by the 1000 Genomes project (phase 1)
1000 Genomes - Low coverage 1kg_lc Variations called by the 1000 Genomes project on low coverage sequence data from 179 unrelated individuals (Pilot 1)
Genotyping chip variants all_chips Variants which have assays on commercial chips held in ensembl
  • Affy GeneChip 500K
Affy_500K Variants from the Affymetrix GeneChip Human Mapping 500K Array Set
  • Affy GenomeWideSNP_6.0
Affy_SNP6 Variants from the Affymetrix Genome-Wide Human SNP Array 6.0
  • HumanOmniExpress
HumanOmniExpress Variants from the Illumina HumanOmniExpress 12v1-1_a whole genome genotyping array
  • Illumina_1M-duo
Illumina_1M-duo Variants from the Illumina Human1M-duo v3 whole genome genotyping array designed for association studies
  • Illumina_Cardio-Metabo_Chip
Cardio-Metabo_Chip Variants from the Illumina Cardio-Metabo_Chip genotyping array designed to target variants of interest for metabolic and cardiovascular disease traits
  • Illumina_CytoSNP12v1
Illumina_CytoSNP12v1 Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis
  • Illumina_ExomeChip
ExomeChip Variants from the Illumina ExomeChip genotyping array designed to target variants within exons
  • Illumina_Human610_Quad
Human610_Quad Variants from the Illumina Human610_Quad v1_B whole genome genotyping array designed for association studies
  • Illumina_Human660W-quad
Illumina_660Q Variants from the Illumina Human660W-quad whole genome genotyping array designed for association studies
  • Illumina_HumanHap550
HumanHap550 Variants from the Illumina Human550 v3.0 whole genome genotyping array designed for association studies
  • Illumina_HumanHap650Y
HumanHap650Y Variants from the Illumina HumanHap650Y v3.0 whole genome genotyping array designed for association studies
  • Illumina_HumanOmni1-Quad
HumanOmni1-Quad Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies
  • Illumina_HumanOmni2.5
HumanOmni2.5 Variants from the Illumina HumanOmni2.5 4v1 whole genome genotyping array designed for association studies
  • Illumina_HumanOmni5
HumanOmni5 Variants from the Illumina HumanOmni5v1 whole genome genotyping array designed for association studies
  • Illumina_ImmunoChip
ImmunoChip Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases
ESP_6500 esp_6500 Variants from the NHLBI Exome Sequencing Project (investigating heart, lung and blood disorders)
All HapMap hapmap Variations which have been assayed by The International HapMap Project [http://hapmap.ncbi.nlm.nih.gov/]
  • HapMap - CEU
hapmap_ceu Variations which have been assayed by The International HapMap Project from CEU individuals
  • HapMap - HCB
hapmap_hcb Variations which have been assayed by The International HapMap Project from HCB individuals
  • HapMap - JPT
hapmap_jpt Variations which have been assayed by The International HapMap Project from JPT individuals
  • HapMap - YRI
hapmap_yri Variations which have been assayed by The International HapMap Project from YRI individuals
Anonymous Korean ind_ak1 Variants genotyped in an anonymous Korean individual
Misha Angrist ind_angrist Variants genotyped in Misha Angrist
Henry Louis Gates Jr ind_gates_jr Variants genotyped in Henry Louis Gates Jr
Henry Louis Gates Sr ind_gates_sr Variants genotyped in Henry Louis Gates Sr
Rosalynn Gill ind_gill Variants genotyped in Rosalynn Gill
Anonymous Irish Male ind_irish Variants genotyped in an anonymous Irish Male
Marjolein Kriek ind_kriek Variants genotyped in Marjolein Kriek
Stephen Quake ind_quake Variants genotyped in Stephen Quake
Saqqaq ind_saqqaq Variants genotyped in a Palaeo-Eskimo Saqqaq individual
Saqqaq HC ind_saqqaq_hc Variants genotyped in a Palaeo-Eskimo Saqqaq individual (high confidence SNPs)
Seong-Jin Kim ind_sjk Variants genotyped in Seong-Jin Kim
ENSEMBL:Venter ind_venter Variants genotyped in Craig Venter
ENSEMBL:Watson ind_watson Variants genotyped in James Watson
YanHang ind_yh Variants genotyped in a Han Chinese individual (YanHuang Project)
All phenotype-associated variants ph_variants Variants that have been associated with a phenotype
  • All ClinVar
ClinVar Variants with ClinVar annotation
  • COSMIC phenotype variants
ph_cosmic Phenotype annotations of somatic mutations found in human cancers from the COSMIC project
  • HGMD-PUBLIC variants
ph_hgmd_pub Variants annotated by HGMD
  • NHGRI catalog phenotype variants
ph_nhgri Variants associated with phenotype data from the NHGRI GWAS catalog [http://www.genome.gov/gwastudies/]
  • OMIM phenotype variants
ph_omim Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database
  • PhenCode
phencode Variants from the PhenCode Project
  • Uniprot phenotype variants
ph_uniprot Variations with phenotype annotations provided by Uniprot
  • clinically associated
clin_assoc Variants described by ClinVar as being probable-pathogenic, pathogenic, drug-response or histocompatibility

Clinical significance

See below the list of the clinical significance terms you can find in the human Ensembl Variation database:

IconValueClinVar exampleDGVa example
associationrs326-
benignrs328nsv491526
confers sensitivityrs1799853-
drug responsers671-
likely benignrs693nsv917620
likely pathogenicrs140603esv1791726
not providedrs661nsv508007
otherrs4220-
pathogenicrs268esv2830397
protectivers671-
risk factorrs333-
uncertain significancers4746esv2830426

Further explanations about the clinical significance terms are available on the ClinVar website.

ClinVar rating

We use the ClinVar "four-star" rating system to indicate the quality of classification/validation of the variant:

RatingDescriptionExample
greygreygreygrey not classified by submitter rs483353044
goldgreygreygrey classified by single submitter rs121908823
goldgoldgreygrey classified by multiple submitters rs112868646
goldgoldgoldgrey reviewed by expert panel rs267608155
goldgoldgoldgold reviewed by professional society rs113993960

Evidence status

We provide a simple summary of the evidence supporting a variant as a guide to its potential reliability

Icon Name Description
Multiple_observations The variant has multiple independent dbSNP submissions, i.e. submissions with a different submitter handles or different discovery samples
Frequency The variant is reported to be polymorphic in at least one sample
HapMap The variant is polymorphic in at least one HapMap panel (human only)
1000 Genomes The variant was discovered in the 1000 genomes project (human only)
Cited The variant is cited in a PubMed article.
ESP The variant was discovered in the Exome Sequencing Project (human only).

Quality control

A quality control process is employed to check imported variation data. Suspect variations and alleles are flagged, but are not withheld from downstream annotation. Data failing the checks is available through the browser where failure reasons are prominently listed. The API does not extract failed data by default, unless the database adaptor is specifically configured to do so using Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::include_failed_variations();

Variations for which dbSNP holds citations from PubMed are not submitted to the QC process so are not flagged as failed.

Failure reasons

QC Type Reported failure reason Checking process
Mapping checks Variation does not map to the genome Variations with flanking sequences which do not map to reference or non-reference genomic sequences are flagged as failed.
Variation maps to more than 1 location For variations with flanking sequences mapping to a reference sequence, the number of mappings within all reference sequences is counted and those mapping more than once are flagged as failed. (Variants with a single mapping to both X and Y within a PAR region are not failed.) For variations with flanking sequences which do not map to a reference sequence, the number of mappings within all non-reference sequences is counted and those mapping more than once are flagged as failed.
Mapped position is not compatible with reported alleles The length of the reported alleles is compared to that expected given the coordinates specified for the variation. If none of the alleles match the expected length, the variation is flagged as failed.
None of the variant alleles match the reference allele The sequence at the coordinates specified for the variation are extracted from the reference genome and compared to the dbSNP refSNP alleles. If the extracted sequence does not match the expected alleles, the variation is flagged as failed.
Checks on the alleles of refSNPs Loci with no observed variant alleles in dbSNP Variations with dbSNP refSNP alleles reported as 'NOVARIATION' are flagged as failed.
Variation has more than 3 different alleles Variations with all of A, T, G and C in the dbSNP refSNP alleles are flagged as failed.
Alleles contain ambiguity codes Variations with a IUPAC ambiguity code (eg. M, Y, R, etc ) in the dbSNP refSNP alleles are reported as failed.
Alleles contain non-nucleotide characters Variations with unexpected characters in the dbSNP refSNP alleles are reported as failed.
Checks on the alleles in dbSNP submissions Additional submitted allele data from dbSNP does not agree with the dbSNP refSNP alleles Alleles from dbSNP submissions ( primarily frequency submissions, but also variant discovery submissions which have been merged in the dbSNP pipeline with the pre-existing refSNP variation) are checked against the dbSNP refSNP alleles and discrepant sets flagged as failed. Often this will highlight a strand error in the submission of frequency information for a known variation. Tradditionally, the failure would be flagged at the variation level, in new database builds it is flagged at the allele submission level.
External failure classification Flagged as suspect by dbSNP Variations reported as being suspect by dbSNP due to being in probable paralogous regions are imported but flagged as failed (human only).
New assembly Variation can not be re-mapped to the current assembly Variations that mapped to the previous assembly, but couldn't be remapped to the current assembly are flagged as failed.